12-129989920-C-T

Variant names:

• chr12-129989920-C-T
• rs1993757

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0327 in 152,252 control chromosomes in the GnomAD database, including 396 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.033 (396 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0920

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0327 AC: 4968 AN: 152134 Hom.: 389 Cov.: 32

Gnomad AFR AF: 0.00492

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.00864

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.0829

Gnomad FIN AF: 0.0580

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00306

Gnomad OTH AF: 0.0406

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0327 AC: 4981 AN: 152252 Hom.: 396 Cov.: 32 AF XY: 0.0406 AC XY: 3020 AN XY: 74432

Gnomad4 AFR AF: 0.00491

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.00864

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.0826

Gnomad4 FIN AF: 0.0580

Gnomad4 NFE AF: 0.00306

Gnomad4 OTH AF: 0.0416

Alfa AF: 0.0312 Hom.: 61

Bravo AF: 0.0379

Asia WGS AF: 0.155 AC: 542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.3
DANN	Benign	0.71

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1993757; hg19: chr12-130474465;